Interactions between proteins and/or their substrates or ligands are critical for normal cell function, physiologic signal transduction, as well as for therapeutic intervention in many pathophysiologic or disease-related processes. Proteins and peptides are capable of adopting compact, well-ordered conformations, and performing complex chemical operations, e.g., catalysis, highly selective recognition, etc. The three dimensional structure is the principal determinant that governs specificity in protein-protein and/or protein-substrate interactions. Thus, the conformation of peptides and proteins is central for their biological function, pharmaceutical efficacy, and their therapeutic preparation.
Protein folding is inextricably linked to function in both proteins and peptides because the creation of an “active site” requires proper positioning of reactive groups. Consequently, there has been a long-felt need to identify synthetic polymer or oligomers, which display discrete and predictable (i.e., stable) folding and oligomerizing propensities (hereinafter referred to as “foldamers”) to mimic natural biological systems. Insofar as these unnatural backbones are resistant to the action of proteases and peptidases, they are useful as probes having constrained conformational flexibility or as therapeutics with improved pharmacological properties, e.g., pharmacokinetic (PK) and/or pharmacodynamics (PD) features, such as potency and/or half-life. Whereas a naturally occurring polypeptide comprised entirely of α-amino acid residues will be readily degraded by any number of proteases and peptidases, foldamers, including chimeras of natural peptides and synthetic amino acid derivatives, mimetics or pseudopeptides, are not.
As noted above, the interest in foldamers stems in part from their resistance to enzymatic degradation. They are also interesting molecules because of their conformational behavior. The elucidation of foldamers having discrete conformational propensities akin to those of natural proteins has led to explorations of peptides constructed from β-, γ-, or δ-amino acids. γ-Peptides containing residues bearing γ-substitution or α, γ-disubstitution or α, β, γ-trisubstitution have been shown to adopt a helical conformation defined by a 14-member turn that is stabilized by C═O(i)→NH(i+3) hydrogen bonds (see FIG. 1c). Both the 314 and 2.512 helical backbones have been found suitable for the design of stabilized helical peptides useful for therapeutic purposes. For example, in order to cluster polar residues on one face of the helix, amphiphilic 314-helical β-peptides have been constructed from hydrophobic-cationic-hydrophobic- or hydrophobic-hydrophobic-cationic residue triads.
The ability to use double H-bonding with disubstituted (thio)ureas as an activation mechanism in catalysis is known. Additionally, disubsituted ureas with electron-withdrawing groups are known to readily form co-crystals with a variety of proton acceptors including carbonyl groups. It has also been shown that highly enantioselective reactions can be promoted by chiral (thio)urea derivatives. The general utility of monofunctional and bifunctional ureas and thioureas as acid catalysts has been intensively explored for the synthesis of enantiomerically enriched molecules.
A number of organocatalysts and processes, including cascade and multicomponent reactions, have been reported to date. Organocatalysts present a number of advantages: they are non-toxic, affordable, easy to handle, and they allow the use of metal-free procedures. However, one of the main drawbacks is the general need for high catalyst loads often comprised between 5-20 mol % which is of course detrimental for applications. Therefore, there is a need to develop more active organic catalysts, able to promote asymmetric chemical transformations in very low loadings. Some have proposed integrating positive cooperativity through folding to enhance catalyst efficiency. That is, preorganizing the catalyst through H-bonding could contribute to cooperative ligand binding, to greater stabilization of charged intermediates, and to minimize the entropic cost of transition state (TS) binding. By using an original turn mimetic structure that populates a well-defined hairpin conformation, conformationally defined, but still flexible thiourea catalysts for asymmetric synthesis can be generated. Currently known bis-thiourea catalysts do not involve intramolecular cooperative H-bonding.
Advance in the design of bioinspired folded systems raises new prospects for protein/nucleic acid mimicry and for the design of architectures with functions beyond that of natural biopolymers. A significant number of building blocks and related oligomers with high propensity for folding into structurally well-defined and ordered 3D architectures have been reported, and which have been termed Foldamers. The ability to precisely control monomer sequences (and appended side chains) in these non-natural systems opens up interesting opportunities for mimicking biopolymer structures and creating systems with new functions, including catalysts.
H-bonds provide a very versatile way to create intrastrand (either local or remote) connections useful to control folding in new oligomeric materials. Non-natural oligoamides represent the quintessential foldamers. The urea group which shares a number of features with the amide linkage, i.e. rigidity, planarity, polarity, and hydrogen bonding capacity is also an interesting linkage for the construction of folded architectures. For example, aliphatic N,N′-linked oligoureas have been developed as helical foldamers.
NMR spectroscopy and X-ray diffraction has been extensively used to characterize the helical conformation of oligoureas. For example, FIGS. 1 shows crystal structures of enantiopure N,N′-linked oligoureas ranging from 5 to 9 urea groups and containing exclusively acyclic residues with proteinogenic side chains. FIG. 1a shows a stereoview of a nona-urea. FIG. 1b shows a view along the helical axis. FIG. 1c shows the detail of the three-centered H-bonding. The similarity between the structures deduced earlier from NMR studies in solution is striking and underlines the excellent complementarities of the two techniques to analyze urea-based foldamers. This also demonstrates the robustness of the folding process, four acyclic residues being sufficient to drive complete helix formation.
Monomeric units with different substitution patterns and various degrees of preorganization may be employed to fine-tune the arrangement of functional groups at the helix surface, modulating the helix stability, and ultimately enabling the design of more effective peptide mimics and/or sophisticated folded architectures.
Foldamer synthesis is not limited to homogenous backbones and approaches based on sequences combining two or more types of monomers, i.e. heterogeneous foldamers. For example, isosteric monomers with proteinogenic side chains of general formula NH—CH(R)—CH2-X—CO, X═CH2, NH, O can be combined to create new heterogeneous helical foldamers within the γ-peptide superfamily. These units are endowed with different folding propensities (U (X═NH)>A (X═CH2)>C(X═O)), the stability of the resulting fold is controlled by the ratio of A, U and C units and by their sequence distribution. Oligomers consisting of 1:1 alternation of U and C (or A) linkages and 2:2 alternations of U and A units retain the ability to fold into well-defined helical structures. Structures at atomic resolution obtained provide guidelines for the design and development of a large ensemble of structurally-related, but chemically distinct helical backbones.